Proc. BioPPN 2012, a satellite event of PETRI NET 2012



     A Database-supported Modular Modelling
    Platform for Systems and Synthetic Biology

                     Mary Ann Blätke and Wolfgang Marwan

   Lehrstuhl für Regulationsbiologie and Magdeburg Centre for Systems Biology,
  Otto-von-Guericke Universität, Universitätsplatz 2, 39106 Magdeburg, Germany
                             maryann.blaetke@ovgu.de



Extended Abstract

Background. Facilitating the handling of the increasing number of kinetic models
is a challenging task in biomodel engineering. Usually advanced mathematical skills
are required to generate, curate, update or to just perform simulations with a kinetic
model. This makes modelling less popular in the life sciences. In addition, an on-going
trend in biomodel engineering is the representation of biological systems in the form
of monolithic models, which are inherently complex due to the numerous interwoven
components. This makes them hardly accessible to others, especially for curation and
updating. Moreover, monolithic models usually cannot be linked without extensive re-
structuring. Therefore, biomodel engineering would benefit from a universal and unify-
ing modelling platform facilitating the use of models and making them more appealing
even for wet lab life scientists.

Results. We developed a modular modelling concept, where modules focus on the re-
actions of each individual protein with its specific interaction partners as described by
a Petri net [1–4]. These Petri net modules are graphically displayed, can be executed
individually and may be coupled with via specific connection interfaces. Our concept
is supported by a prototype database with a publically accessible web-interface [1].
In addition to the network structure of each module, the database contains metadata
for documentation purposes. Therefore, each module corresponds to a wiki-like minire-
view. The database can manage multiple versions of each module. The organization
of molecule-oriented modules in a database facilitates the automatic composition into
coherent models containing an arbitrary number of molecular species chosen ad hoc
by the user. Petri nets composed from modules can be executed as ODEs, stochastic,
hybrid, or merely qualitative models and exported in SMBL format.

Conclusion. The modular modelling concept and its extension by a supportive database,
facilitates the curation, documentation, version control, and update of individual mod-
ules and the subsequent automatic composition of complex models, without requiring
mathematical skills [1–4]. Modules can be recombined according to user-defined sce-
narios, e.g., considering the gene expression patterns in given cell types, under certain
physiological conditions, or states of disease. As synthetic biology application we pro-
pose we propose the fully automated generation of synthetic or synthetically rewired
network models by composition of metadata-guided automatically modified modules
representing altered protein binding sites.




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            Proc. BioPPN 2012, a satellite event of PETRI NET 2012



References
1. Blätke, M.A., Dittrich, A., Rohr, C., Heiner, M., Schaper, F., Marwan, W.:
   JAK/STAT signalling - an executable model assembled from molecule-centred mod-
   ules demonstrating a module-oriented database concept for systems- and synthetic
   biology. submitted (2012)
2. Blätke, M.A., Heiner, M., Marwan, W.: Predicting Phenotype from Genotype
   Through Automatically Composed Petri Nets. submitted (2012)
3. Blätke, M., Meyer, S., Marwan, W.: Pain signaling - a case study of the modular petri
   net modeling concept with prospect to a protein-oriented modeling platform. In:
   Proc. of the International Workshop on Biological Processes & Petri Nets (BioPPN),
   satellite event of Petri Nets 2011. CEUR Workshop Proceedings, vol. 724, pp. 117–
   134. CEUR-WS.org (June 2011)
4. Blätke, M., Meyer, S., Stein, C., Marwan, W.: Petri net modeling via a modular
   and hierarchical approach applied to nociception. In: Proc. International Workshop
   on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010.
   pp. 131–143. ISBN: 978-972-8692-53-7 (June 2010)




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